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Mauricio Carneiro f0c81b59b0 Implementation of the new BQSR plotting infrastructure 
* removed low quality bases from the recalibration report.
   * refactored the Datum (Recal and Accuracy) class structure
   * created a new plotting csv table for optimized performance with the R script
   * added a datum object that carries the accuracy information (AccuracyDatum) for plotting
   * added mean reported quality score to all covariates
   * added QualityScore as a covariate for plotting purposes
   * added unit test to the key manager to operate with one required covariate and multiple optional covariates
   * integrated the plotting into BQSR (automatically generates the pdf with the recalibration tearsheet)
 		2012-04-17 19:23:55 -04:00
..
R Improve variantCallQC.R 2012-04-13 17:00:37 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
doc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
java Implementation of the new BQSR plotting infrastructure 2012-04-17 19:23:55 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala AggregateMetrics: 2012-04-17 11:45:32 -04:00
testdata continuing the BQSR triage... 2012-04-05 14:34:15 -04:00